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Re: [Freesurfer] Freeview problems

Error using mris_transform in...

Savoia, Alice (Stud. FPN)

15 Apr 2024 15 Apr '24

10:36 a.m.

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Wang, Ruopeng

15 Apr 15 Apr

10:40 a.m.

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nlmailto:a.savoia@student.maastrichtuniversity.nl> wrote:

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To whom it may concern, I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place. Thank you for your help, Best regards. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Savoia, Alice (Stud. FPN)

10:42 a.m.

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Is in the freesurfer directory ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@MGH.HARVARD.EDU Sent: Monday, April 15, 2024 4:40 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problems

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nlmailto:a.savoia@student.maastrichtuniversity.nl> wrote:

External Email - Use Caution

To whom it may concern, I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place. Thank you for your help, Best regards. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1bq9Xqn_Xr10GqKbjHWmlUGRPGo8mgepDHTL0hecq1gx-yo...

Huang, Yujing

10:44 a.m.

Can you try 'mri_info <input.mgz> --voxel 0 0 0'? Just wanted to make sure the license file is read properly.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Savoia, Alice (Stud. FPN) Sent: Monday, April 15, 2024 10:42 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution Is in the freesurfer directory ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> Sent: Monday, April 15, 2024 4:40 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problems

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nlmailto:a.savoia@student.maastrichtuniversity.nl> wrote:

External Email - Use Caution To whom it may concern, I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place. Thank you for your help, Best regards. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1bq9Xqn_Xr10GqKbjHWmlUGRPGo8mgepDHTL0hecq1gx-yoVUj6MUeI0bQsmw55rXBWei3mW3sJ0LEL8aDCnJhTK-mc1Xxg8E6XT1jqvs7dv7Mxcl0cwvpklc-_fe8sKR4ljnXXogcRfpo0QtsFdkK8LJD9Xja0ORIUIjUV55mhBGqdt56jrdAxMbWPHk5xVTvu32Zs6sNeH17ufdIzb9YkYzrTQNU63AmW_anCWsQpBUMTs8OgL0VDOXAe5BJF-RfJXefrkakHwwxFJLHPIrN-XJ7UHc3zsU8OlahiPLDe5Y6SkGS7ZOFWr0XCnkViep/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Savoia, Alice (Stud. FPN)

11:02 a.m.

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I think is not reading it properly because it gives an error, also I tried to setup the environment on the terminal but is not working either

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@MGH.HARVARD.EDU Sent: Monday, April 15, 2024 4:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problems

Can you try ‘mri_info <input.mgz> --voxel 0 0 0’? Just wanted to make sure the license file is read properly.

Best,

Yujing

External Email - Use Caution

Is in the freesurfer directory

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> Sent: Monday, April 15, 2024 4:40 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problems

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nlmailto:a.savoia@student.maastrichtuniversity.nl> wrote:

External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place.

Thank you for your help,

Best regards.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1X3IfxY-YiB2AxIU-xCvC6G2WVhl1mBRg__1IkmPGHHNlqG...https://secure-web.cisco.com/1bq9Xqn_Xr10GqKbjHWmlUGRPGo8mgepDHTL0hecq1gx-yoVUj6MUeI0bQsmw55rXBWei3mW3sJ0LEL8aDCnJhTK-mc1Xxg8E6XT1jqvs7dv7Mxcl0cwvpklc-_fe8sKR4ljnXXogcRfpo0QtsFdkK8LJD9Xja0ORIUIjUV55mhBGqdt56jrdAxMbWPHk5xVTvu32Zs6sNeH17ufdIzb9YkYzrTQNU63AmW_anCWsQpBUMTs8OgL0VDOXAe5BJF-RfJXefrkakHwwxFJLHPIrN-XJ7UHc3zsU8OlahiPLDe5Y6SkGS7ZOFWr0XCnkViep/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Huang, Yujing

11:05 a.m.

Can you set the terminal output?

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Savoia, Alice (Stud. FPN) Sent: Monday, April 15, 2024 11:03 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution I think is not reading it properly because it gives an error, also I tried to setup the environment on the terminal but is not working either

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: Monday, April 15, 2024 4:44 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problems

Can you try 'mri_info <input.mgz> --voxel 0 0 0'? Just wanted to make sure the license file is read properly.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Savoia, Alice (Stud. FPN) Sent: Monday, April 15, 2024 10:42 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution

Is in the freesurfer directory

________________________________

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nlmailto:a.savoia@student.maastrichtuniversity.nl> wrote:

External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place.

Thank you for your help,

Best regards.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1bq9Xqn_Xr10GqKbjHWmlUGRPGo8mgepDHTL0hecq1gx-yoVUj6MUeI0bQsmw55rXBWei3mW3sJ0LEL8aDCnJhTK-mc1Xxg8E6XT1jqvs7dv7Mxcl0cwvpklc-_fe8sKR4ljnXXogcRfpo0QtsFdkK8LJD9Xja0ORIUIjUV55mhBGqdt56jrdAxMbWPHk5xVTvu32Zs6sNeH17ufdIzb9YkYzrTQNU63AmW_anCWsQpBUMTs8OgL0VDOXAe5BJF-RfJXefrkakHwwxFJLHPIrN-XJ7UHc3zsU8OlahiPLDe5Y6SkGS7ZOFWr0XCnkViep/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Savoia, Alice (Stud. FPN)

11:12 a.m.

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Ok I tried again and when I inserted the mri_info... the output was "mri_info: could not parse extension from 0" ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@MGH.HARVARD.EDU Sent: Monday, April 15, 2024 4:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problems

Can you try ‘mri_info <input.mgz> --voxel 0 0 0’? Just wanted to make sure the license file is read properly.

Best,

Yujing

External Email - Use Caution

Is in the freesurfer directory

________________________________

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nlmailto:a.savoia@student.maastrichtuniversity.nl> wrote:

External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place.

Thank you for your help,

Best regards.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1m4fLSvoBjBYpugs5TeMDpzFv2iuxHMN_-vYsjxEfutCvLa...https://secure-web.cisco.com/1bq9Xqn_Xr10GqKbjHWmlUGRPGo8mgepDHTL0hecq1gx-yoVUj6MUeI0bQsmw55rXBWei3mW3sJ0LEL8aDCnJhTK-mc1Xxg8E6XT1jqvs7dv7Mxcl0cwvpklc-_fe8sKR4ljnXXogcRfpo0QtsFdkK8LJD9Xja0ORIUIjUV55mhBGqdt56jrdAxMbWPHk5xVTvu32Zs6sNeH17ufdIzb9YkYzrTQNU63AmW_anCWsQpBUMTs8OgL0VDOXAe5BJF-RfJXefrkakHwwxFJLHPIrN-XJ7UHc3zsU8OlahiPLDe5Y6SkGS7ZOFWr0XCnkViep/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Huang, Yujing

11:27 a.m.

I don't think you pass the arguments correctly to mri_info. You need to specify an input image - 'mri_info input.mgz --voxel 0 0 0'.

This should be done after you have sourced Freesurfer environment correctly. Here are the instructions to setup your environment on Mac https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac

Also, which version of Freesurfer you are using?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Savoia, Alice (Stud. FPN) Sent: Monday, April 15, 2024 11:12 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution Ok I tried again and when I inserted the mri_info... the output was "mri_info: could not parse extension from 0" ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: Monday, April 15, 2024 4:44 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problems

Can you try 'mri_info <input.mgz> --voxel 0 0 0'? Just wanted to make sure the license file is read properly.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Savoia, Alice (Stud. FPN) Sent: Monday, April 15, 2024 10:42 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution

Is in the freesurfer directory

________________________________

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nlmailto:a.savoia@student.maastrichtuniversity.nl> wrote:

External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place.

Thank you for your help,

Best regards.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1bq9Xqn_Xr10GqKbjHWmlUGRPGo8mgepDHTL0hecq1gx-yoVUj6MUeI0bQsmw55rXBWei3mW3sJ0LEL8aDCnJhTK-mc1Xxg8E6XT1jqvs7dv7Mxcl0cwvpklc-_fe8sKR4ljnXXogcRfpo0QtsFdkK8LJD9Xja0ORIUIjUV55mhBGqdt56jrdAxMbWPHk5xVTvu32Zs6sNeH17ufdIzb9YkYzrTQNU63AmW_anCWsQpBUMTs8OgL0VDOXAe5BJF-RfJXefrkakHwwxFJLHPIrN-XJ7UHc3zsU8OlahiPLDe5Y6SkGS7ZOFWr0XCnkViep/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Savoia, Alice (Stud. FPN)

17 Apr 17 Apr

3:40 a.m.

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The thing is that I am specifying the image. I am using the latest version of freesurfer

Inviato da Outlook per Androidhttps://secure-web.cisco.com/1W7yKqhfJwWOUYl3f6U4jF_oYFNwM-CC21FOzRUbLSIPEBPoWwmd8-mxshlcJOSclq0tAlPTaIAdAsZq1pZNxBvMKYYu7Si7dhVSLlXC4THNVPUr5ZuxMnVCJSANKiPcCWFkUTSNUrMqzsaNXOQVRhwIM9rMUCxBRvKivRiAwgcz6ZVAUdhctB5r_Rq6Mm1P0c8dtBJ6nZ_LoMlz6PnxC5WilYWMlsa1V7k2vrtfK6NCqnviBLFrBjX-TxBxHwszt5ABV4IhkMrJvJRynXmYkgvehqcN0fjU-a-A22OmH1n-dvvgb8BXRHLWw3UkClctqChhJYVjYmctl8MnySJY0_Q/https%3A%2F%2Faka.ms%2FAAb9ysg ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Monday, April 15, 2024 5:27:35 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problems

I don’t think you pass the arguments correctly to mri_info. You need to specify an input image – ‘mri_info input.mgz --voxel 0 0 0’.

This should be done after you have sourced Freesurfer environment correctly. Here are the instructions to setup your environment on Mac https://secure-web.cisco.com/1rDKNPfMnebEaPcslhVYc4x92ni2r-ZJVCYbzp7uAEUT-O0...

Also, which version of Freesurfer you are using?

Best,

Yujing

External Email - Use Caution

Ok I tried again and when I inserted the mri_info... the output was "mri_info: could not parse extension from 0"

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: Monday, April 15, 2024 4:44 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problems

Can you try ‘mri_info <input.mgz> --voxel 0 0 0’? Just wanted to make sure the license file is read properly.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Savoia, Alice (Stud. FPN) Sent: Monday, April 15, 2024 10:42 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problems

External Email - Use Caution

Is in the freesurfer directory

________________________________

Can you confirm where your license file is?

Ruopeng

On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nlmailto:a.savoia@student.maastrichtuniversity.nl> wrote:

External Email - Use Caution

To whom it may concern,

I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place.

Thank you for your help,

Best regards.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XiK9iIDyiyxnVIxS_tbwQMQmXBqvWqTREAzVFiEqbHPRrj...https://secure-web.cisco.com/1bq9Xqn_Xr10GqKbjHWmlUGRPGo8mgepDHTL0hecq1gx-yoVUj6MUeI0bQsmw55rXBWei3mW3sJ0LEL8aDCnJhTK-mc1Xxg8E6XT1jqvs7dv7Mxcl0cwvpklc-_fe8sKR4ljnXXogcRfpo0QtsFdkK8LJD9Xja0ORIUIjUV55mhBGqdt56jrdAxMbWPHk5xVTvu32Zs6sNeH17ufdIzb9YkYzrTQNU63AmW_anCWsQpBUMTs8OgL0VDOXAe5BJF-RfJXefrkakHwwxFJLHPIrN-XJ7UHc3zsU8OlahiPLDe5Y6SkGS7ZOFWr0XCnkViep/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Huang, Yujing
Savoia, Alice (Stud. FPN)
Wang, Ruopeng